Set specular map from alpha channel
For your first question, to stop your diffuse texture from using the alpha channel of the image, go to the Texture tab and under Image, untick Use  Alpha.

Here is how it looks now as compared to those above.



If you tick Specular under Influence, Blender will automatically use any specular highlights in the image .

Additionally, you can check parts of your textures you want to be affected and or by how much under Influence in the same texture tab.